1. The hot end fan, print cooling fan and the heater share a common +ve connection. That's the 4 pins with the orange square around it in your diagram, This is no problem, assuming that you are not trying to run them from different voltages. You can connect those 4 wires to the VIN side of the E0 terminal block. Caution! On most Duet PCB revisions, the E0- and VIN labels on those pins are the wrong way round. The VIN side of the 2-pin terminal block is nearest the edge of the board that has the USB connector and SD card. Then you can wire the heater- connection to the other pin of the E0 terminal block, and the print cooling fan negative terminal (which you marked with a yellow line) to the Fan- pin on the FAN0 connector.

2. The hot end fan negative terminal, thermistor ground wire and endstop switch ground wire share a common pin (bottom left pin in your diagram). This is poor design, because it will affect the accuracy of the temperature reading at higher temperatures, and if the wire breaks then it will feed 12V or 24v via the fan into the thermistor input and the endstop input. So my recommendation is that you replace this by 3 separate wires (then you would also be able to control the hot end cooling fan thermostatically). But if you want to try a common ground, you can connect it to the ground pin of the X endstop connector. Then the other X endstop connector wire goes to the STP pin on the same connector, and the thermistor wire goes to the E0 R(th) pin of the thermistor connector.